Antibiotics for gardens and forests: Part I

The title of a recent paper in the Journal of the American Chemical Society, or JACS for short, is: Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Non-ribosomal Lipopeptides Featuring a Transient Amino Acid Building Block. JACS publishes heavy stuff. Readers may think these authors and JACS are on a one-lane road to obscurity, but there is substance here. A shorter title might have been Antibiotics from Pseudomonas Kill Nasty Amoebae and Fungi. The authors named the class of antibiotics after Keanu Reeves, the Canadian actor who plays retired assassin, John Wick, who emerges to kill bad guys. Amoebae and fungi cause many diseases, and they are all bad guys because forestry, agriculture, and medicine have few defenses against them. Fungi kill our crops and trees in periodic waves. I want our ash, chestnut, hemlock, and elm trees back, or at least to give them a fighting chance.

The Jena people, led by Dr. Pierre Stallforth, use a strategy that lets evolution do much of the work. They looked for antibiotics in biological situations where two or more species have fallen into an equilibrium, a condition called either mutualism or competition. They reasoned that one species may make an antibiotic or natural product to compete.

Amoeba-like cells have a lot of internal architecture: vacuoles, nuclei, sites to make special proteins, structures to carry out tasks of digestion and energy production, and ways to recognize harmful bacteria and pull them inside. These cells crawl over the surface of our lungs, peritoneum, and kidneys. They clean up bacteria and debris after inflammation. In the lungs they are called alveolar macrophages, but they patrol almost everywhere. All higher organisms have amoebae or similar cells; they are an essential cellular life form that evolution has kept. Some amoebae can also cause disease; think of amoebic dysentery or the brain destroying amoebae that people get in warm freshwater ponds.

Some amoebae live in a special vacuole, surrounded by a membrane, where they have acquired the ability to interrupt a process that normally kills them. Mycobacterium tuberculosis and Legionella pneumoniae live in such cellular compartments, where they grow and divide. The Stallforth lab uses a species called Dictyostelium discoideum that lives in soil and eats the many bacteria they find there. Legionella and TB bacteria flourish in Dictyostelium the vacuoles of these amoebae.

Your columnist and his lab studied Dictyostelium for decades and wrote a book on these shapeshifting, complicated, and quite beautiful creatures. Type ‘John Bonner and Princeton’ into a browser and you will find a lovely film, made in 1947. Albert Einstein asked to see it. There is more to this story, but let’s return to Dr. Stallworth.

Instead of isolating bacteria or amoebae from this niche and asking if individual bacteria or amoebae produced antibiotics, they extracted DNA and examined the sequences of A, C, G, and T of millions of individual genes. It sounds hard, and it was once, but now the process is efficient and automated. Two classes of genes make the enzymes to produce antibiotics, each easily recognized by their DNA sequences stored in enormous databases. The group found one of them in the bacteria called Pseudomonas.

The story of our niche takes us back to the experimental forest of the University of Virginia in the Great Smoky Mountains, where, in 2014, evolutionary biologists Joan Strassmann and David Quellar of Washington University were looking for new strains of Dictyostelium.

Joan found a fruiting body of Dictyostelium, which looks like a lollipop about 1mm high, but it was on a steaming pile of deer scat. Where the business end of the lollipop would be, there was a ball of tough spores, about 50,000 held in a drop by surface tension. Fruiting bodies form in the lab, but that was the first time one had been seen in the wild. In the liquid around the spores there were bacteria, a strain of Pseudomonas, now called QS1027 (Queller-Strassmann), that we now know secretes antibiotics.

Let me leave you with Professor Joan Strassmann, author of a recent book called Slow Birding, a member of The National Academic of Sciences, a teacher and mentor, on hands and knees with her nose six inches from a heap of deer poop, yelling in delight. Joy is where you find it.

Richard Kessin, Ph.D, is Emeritus Professor of Pathology and Cell Biology in the Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical center. His columns are at RichardKessin.com.

The views expressed here are not necessarily those of The Lakeville Journal and The Journal does not support or oppose candidates for public office.

Latest News

To mow or not to mow?

To mow or not to mow?

A partially mowed meadow in early spring provides habitat for wildlife while helping to keep invasive plants in check.

Dee Salomon

Love it or hate it, there is no denying the several blankets of snow this winter were beautiful, especially as they visually muffled some of the damage they caused in the first place.There appears to be tree damage — some minor and some major — in many places, and now that we can move around, the pre-spring cleanup begins. Here, a heavy snow buildup on our sun porch roof crashed onto the shrubs below, snapping off branches and cleaving a boxwood in half, flattening it.

The other area that has been flattened by the snow is the meadow, now heading into its fourth year of post-lawn alterations. A short recap on its genesis: I simply stopped mowing a half-acre of lawn, planted some flowering plants, spread little bluestem seeds and, far less simply, obsessively pluck out invasive plants such as sheep sorrel and stilt grass. And while it’s not exactly enchanting, it is flourishing, so much so that I cannot bring myself to mow.

Keep ReadingShow less

Where the mat meets the market

Where the mat meets the market

Kathy Reisfeld

Elena Spellman

In a barn on Maple Avenue in Great Barrington, Kathy Reisfeld merges two unlikely worlds: wealth management and yoga, teaching clients and students alike how stability — financial and emotional — comes from practice.

Her life sits at an intersection many assume can’t exist: high finance and yoga. One world is often reduced to greed, the other to “woo-woo” stretching. Yet in conversation, she makes both feel grounded, less like opposites and more like two languages describing the same human need for stability.

Keep ReadingShow less
Capitol hosts first-ever staging of Civil War love story

Playwright Cinzi Lavin, left, poses with Kathleen Kelly, director of ‘A Goodnight Kiss.’

Jack Sheedy

Litchfield County playwright Cinzi Lavin’s “A Goodnight Kiss,” based on letters exchanged between a Civil War soldier and the woman who became his wife, premiered in 2025 to sold-out audiences in Goshen, where the couple once lived. Now the original cast, directed by Goshen resident Kathleen Kelly, will present the play beneath the gold dome of Connecticut’s Capitol in Hartford as part of the state’s America250 commemoration — marking what organizers believe may be the first such performance at the Capitol.

“I don’t believe any live performances of an actual play (at the Capitol) have happened,” said Elizabeth Conroy, administrative assistant at the Office of Legislative Management, who coordinates Capitol events.

Keep ReadingShow less
google preferred source

Want more of our stories on Google? Click here to make us a Preferred Source.

Hunt Library launches VideoWall for filmmakers

Yonah Sadeh, Falls Village filmmaker and curator of David M. Hunt Library’s new VideoWall.

Robin Roraback

The David M. Hunt Library in Falls Village, known for promoting local artists with its ArtWall, is debuting a new feature showcasing filmmakers. The VideoWall will premiere Saturday, March 28, at 6 p.m. with a screening of two short films by Brooklyn-based documentary filmmaker and animator Imogen Pranger.

The VideoWall is the idea of Falls Village filmmaker Yonah Sadeh, who also serves as curator. “I would love the VideoWall to become a place that showcases the work of local filmmakers, and I hope that other creatives in the area will submit their work to be shown,” he said.

Keep ReadingShow less

A bowl full of stars

A bowl full of stars

A bowl full of stones.

Cheryl Heller

There’s a bowl in my studio where pieces of the planet reside. I bring them home from travels, picking them up not for their beauty or distinction but for their provenance. I choose the ones that speak to me — the ones next to pyramids, along hiking trails, on city sidewalks or volcanic slopes.

I like how stones feel in my hand: weighty, grounding. I don’t mind them making my pockets and suitcase heavier. The bowl is about the size of an average carry-on. It has been years since it was light enough for me to lift.

Keep ReadingShow less
One-woman show brings Mumbet’s fight for freedom to Scoville Library
One-woman show brings Mumbet’s fight for freedom to Scoville Library
One-woman show brings Mumbet’s fight for freedom to Scoville Library

On March 29, writer, producer and director Tammy Denease will embody the life and story of Elizabeth Freeman, widely known as Mumbet, in two performances at the Scoville Library in Salisbury. Presented by Scoville Library and the Salisbury Association Historical Society, the performance is part of Salisbury READS, a community-wide engagement with literature and civic dialogue.

Mumbet was the first enslaved woman in Massachusetts to sue successfully for her freedom in 1781. Her victory helped lay the legal groundwork for the abolition of slavery in the state just two years later. In bringing Mumbet’s story to life, Denease does more than reenact history.

Keep ReadingShow less
google preferred source

Want more of our stories on Google? Click here to make us a Preferred Source.

google preferred source

Want more of our stories on Google? Click here to make us a Preferred Source.